GapMind for catabolism of small carbon sources

 

Aligments for a candidate for H281DRAFT_01112 in Dinoroseobacter shibae DFL-12

Align deoxynucleoside transporter, permease component 2 (characterized)
to candidate 3607107 Dshi_0529 Monosaccharide-transporting ATPase (RefSeq)

Query= reanno::Burk376:H281DRAFT_01112
         (364 letters)



>lcl|FitnessBrowser__Dino:3607107 Dshi_0529
           Monosaccharide-transporting ATPase (RefSeq)
          Length = 333

 Score =  275 bits (703), Expect = 1e-78
 Identities = 140/314 (44%), Positives = 202/314 (64%)

Query: 51  EWFTVALIVVTCLIVGAINPRFFQFATLFDLLHSATTMSLFALGTLVVLASGGIDVSFTA 110
           E     +I++ C +    +PRF    T+ DLL ++  + + A+G ++VL SGGIDVSFTA
Sbjct: 14  ETLVAGVIMLFCFVATVSDPRFLTITTVSDLLRASIVIGILAVGAMLVLVSGGIDVSFTA 73

Query: 111 IAALTMYGITKAVFAWWPDAPFALILVTGALGGVVLGMVNGLLVHRLKAPSLIVTIGTQY 170
           IA   MY  T      WP+ P+ +I V   + G  LG +NG  +  L  P+LIVT+GT  
Sbjct: 74  IAVFAMYSSTVLSLTIWPEIPWPVIFVISVVFGAALGAINGFFIAFLGLPTLIVTLGTLS 133

Query: 171 LYRGLLLTFIGTTFFMNIPHSMDRFGRIPLFFYHTADGLRAVLPVSVLALVAAAVVTWWL 230
           ++RG LLTFIG+    ++P SM  F R  +    T  G    +P + LAL+   V+TW++
Sbjct: 134 IFRGFLLTFIGSQRISDLPPSMRDFSRGVIARGTTEAGNFYSIPWAALALLFVIVLTWFI 193

Query: 231 LNRTMMGRAVYAMGGSLAIAERLGYNLRAIHLFVFGYTGMLAGIAGILHVSNNRLANPFD 290
           L +TM+GR++YA+GGS+  A R+G N++    FV+ Y G LAG+AGI+H S  R+A+PF 
Sbjct: 194 LKKTMLGRSIYAIGGSVESARRIGINVKWTQFFVYVYVGALAGLAGIIHGSVGRMADPFS 253

Query: 291 LVGSELDVIAAVILGGARITGGTGTVVGTLLGVVLVTLIKSVLILVGVPSTWQKVIIGAF 350
           LVG EL VIAAV+LGGAR+ GG GT+ GT+LGV L+ ++++ LI++G+P+TWQ V IG  
Sbjct: 254 LVGLELSVIAAVVLGGARLIGGYGTLTGTMLGVALIVIVQNSLIVIGIPTTWQSVTIGIL 313

Query: 351 ILLAGTLFALQRKR 364
           ILL   + A + KR
Sbjct: 314 ILLGTGVPAYRAKR 327


Lambda     K      H
   0.328    0.141    0.426 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 339
Number of extensions: 22
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 364
Length of database: 333
Length adjustment: 29
Effective length of query: 335
Effective length of database: 304
Effective search space:   101840
Effective search space used:   101840
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory